Sun Oct 9 03:16:32 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 03:16:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5332695 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 0.5332695 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.9890 centred at (gu) : 90.11621 91.25140 88.30544 assigned negative charge : -647.9938 centred at (gu) : 90.11098 91.22879 88.33013 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8220 nv = 96 ne = 84 npr = 94601 no. pairs analyzed = 94601 no. exposed pairs = 5817 no. arc points = 39660 no. surface atoms = 1952 nbur = 2607 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 330 mr = 4285 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3908 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3524276E-09 3.9466333E-10 midg,1,midg; midg,igrid,midg 4.4766404E-10 1.1926495E-09 1,midg,midg; igrid,midg,midg 6.8875733E-10 7.9300017E-10 gauss-seidel spectral radius is 0.9819936 estimated iterations to convergence 61 setup time was (sec) 0.5000000 now iterating at: 03:16:33 rms-change max change #iterations 8.3068833E-02 12.65049 at 10iterations 8.0362344E-03 1.417458 at 20iterations 2.3187522E-03 0.3387127 at 30iterations 8.9398207E-04 0.1356869 at 40iterations 3.5191944E-04 5.3850174E-02 at 50iterations finished qdiffx linear iterations at : 03:16:36 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.5191944E-04 5.3850174E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:16:36 3.497u 0.157s 0:03.92 92.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 03:16:36 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.599808 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 1.599808 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.9890 centred at (gu) : 90.34679 93.75267 84.91492 assigned negative charge : -647.9938 centred at (gu) : 90.33255 93.68578 84.99017 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 91946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39660 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28259 mr = 63171 m= 2967 mr = 19054 m= 81 mr = 1411 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 0.4600000 number of dielectric boundary points 39610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 32956 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5332695 object centre at (A) : 27.63000 34.10200 199.1430 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3976278E-02 1.8353919E-03 midg,1,midg; midg,igrid,midg 1.9144559E-02 1.3686505E-02 1,midg,midg; igrid,midg,midg 3.3900626E-02 1.2324229E-02 gauss-seidel spectral radius is 0.9982672 estimated iterations to convergence 191 setup time was (sec) 0.6800000 now iterating at: 03:16:37 rms-change max change #iterations 4.021613 177.0773 at 10iterations 1.702768 52.20714 at 20iterations 0.7255413 24.86143 at 30iterations 0.3095140 9.709741 at 40iterations 0.1322961 3.856343 at 50iterations 5.7182789E-02 1.733917 at 60iterations 2.4991419E-02 0.7931519 at 70iterations 1.1405574E-02 0.3787155 at 80iterations 5.7081901E-03 0.1959915 at 90iterations 3.2358808E-03 0.1180191 at 100iterations 2.0610627E-03 7.2783470E-02 at 110iterations 1.4167400E-03 4.6422958E-02 at 120iterations finished qdiffx linear iterations at : 03:16:44 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.4167400E-03 4.6422958E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 03:16:45 7.960u 0.188s 0:08.51 95.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 03:16:45 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4559 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1107 has a net charge of 1.4000 !!! WARNING: FE 2 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.399713 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -4.088000 59.34800 ymin,ymax (A): 0.7229999 67.48100 zmin,zma (A): 169.0660 229.2200 x,y,z range (A): 63.43600 66.75800 60.15401 scale (grids/A): 2.399713 object centre (A): 27.63000 34.10200 199.1430 number of atom coordinates read : 4559 total number of charged atoms : 4326 net assigned charge : 19.99999 assigned positive charge : 667.9890 centred at (gu) : 90.51971 95.62836 82.37186 assigned negative charge : -647.9938 centred at (gu) : 90.49872 95.52846 82.48513 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 214053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39660 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 98373 mr = 155191 m= 27675 mr = 77084 m= 4462 mr = 20273 m= 284 mr = 2813 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 4133 time to turn everything in is 1.120000 number of dielectric boundary points 89371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 34543 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.599808 object centre at (A) : 27.63000 34.10200 199.1430 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2291017 -5.1526960E-02 midg,1,midg; midg,igrid,midg 0.2934771 0.1710578 1,midg,midg; igrid,midg,midg 0.4763467 5.9275996E-02 gauss-seidel spectral radius is 0.9992025 estimated iterations to convergence 280 setup time was (sec) 1.370000 now iterating at: 03:16:46 rms-change max change #iterations 10.42728 306.7897 at 10iterations 6.021690 135.8964 at 20iterations 3.458488 71.92467 at 30iterations 1.978051 37.98965 at 40iterations 1.124926 23.29078 at 50iterations 0.6384538 12.13523 at 60iterations 0.3627599 6.790384 at 70iterations 0.2056440 3.610767 at 80iterations 0.1160690 1.952043 at 90iterations 6.5710507E-02 1.150642 at 100iterations 3.7138049E-02 0.6997070 at 110iterations 2.0974733E-02 0.3600922 at 120iterations 1.1899650E-02 0.2107849 at 130iterations 6.7948424E-03 0.1192131 at 140iterations 3.9190622E-03 7.4445724E-02 at 150iterations 2.3060117E-03 3.9489746E-02 at 160iterations 1.4023960E-03 2.6959419E-02 at 170iterations 9.0209913E-04 1.8173218E-02 at 180iterations finished qdiffx linear iterations at : 03:16:58 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 9.0209913E-04 1.8173218E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 03:16:59 13.225u 0.200s 0:13.90 96.5% 0+0k 0+0io 0pf+0w